| Year |
Citation |
Score |
| 2023 |
Lorenzetti APR, Kusebauch U, Zaramela LS, Wu WJ, de Almeida JPP, Turkarslan S, L G de Lomana A, Gomes-Filho JV, Vêncio RZN, Moritz RL, Koide T, Baliga NS. A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon. Msystems. e0081622. PMID 36912639 DOI: 10.1128/msystems.00816-22 |
0.371 |
|
| 2020 |
López García de Lomana A, Kusebauch U, Raman AV, Pan M, Turkarslan S, Lorenzetti APR, Moritz RL, Baliga NS. Selective Translation of Low Abundance and Upregulated Transcripts in Halobacterium salinarum. Msystems. 5. PMID 32723790 DOI: 10.1128/mSystems.00329-20 |
0.324 |
|
| 2020 |
Arrieta-Ortiz ML, Hafemeister C, Shuster B, Baliga NS, Bonneau R, Eichenberger P. Inference of Bacterial Small RNA Regulatory Networks and Integration with Transcription Factor-Driven Regulatory Networks. Msystems. 5. PMID 32487739 DOI: 10.1128/mSystems.00057-20 |
0.311 |
|
| 2020 |
Peterson EJR, Abidi AA, Arrieta-Ortiz ML, Aguilar B, Yurkovich JT, Kaur A, Pan M, Srinivas V, Shmulevich I, Baliga NS. Intricate Genetic Programs Controlling Dormancy in Mycobacterium tuberculosis. Cell Reports. 31: 107577. PMID 32348771 DOI: 10.1016/J.Celrep.2020.107577 |
0.377 |
|
| 2019 |
Peterson EJ, Bailo R, Rothchild AC, Arrieta-Ortiz ML, Kaur A, Pan M, Mai D, Abidi AA, Cooper C, Aderem A, Bhatt A, Baliga NS. Path-seq identifies an essential mycolate remodeling program for mycobacterial host adaptation. Molecular Systems Biology. 15: e8584. PMID 30833303 DOI: 10.15252/Msb.20188584 |
0.308 |
|
| 2018 |
Otwell AE, López García de Lomana A, Gibbons SM, Orellana MV, Baliga NS. Systems biology approaches towards predictive microbial ecology. Environmental Microbiology. PMID 30106224 DOI: 10.1111/1462-2920.14378 |
0.328 |
|
| 2018 |
Ament SA, Pearl JR, Cantle JP, Bragg RM, Skene PJ, Coffey SR, Bergey DE, Wheeler VC, MacDonald ME, Baliga NS, Rosinski J, Hood LE, Carroll JB, Price ND. Transcriptional regulatory networks underlying gene expression changes in Huntington's disease. Molecular Systems Biology. 14: e7435. PMID 29581148 DOI: 10.15252/Msb.20167435 |
0.568 |
|
| 2017 |
Qin W, Amin SA, Lundeen RA, Heal KR, Martens-Habbena W, Turkarslan S, Urakawa H, Costa KC, Hendrickson EL, Wang T, Beck DA, Tiquia-Arashiro SM, Taub F, Holmes AD, Vajrala N, ... ... Baliga NS, et al. Stress response of a marine ammonia-oxidizing archaeon informs physiological status of environmental populations. The Isme Journal. PMID 29053148 DOI: 10.1038/Ismej.2017.186 |
0.328 |
|
| 2017 |
López García de Lomana A, Kaur A, Turkarslan S, Beer KD, Mast FD, Smith JJ, Aitchison JD, Baliga NS. Adaptive Prediction Emerges Over Short Evolutionary Time Scales. Genome Biology and Evolution. 9: 1616-1623. PMID 28854640 DOI: 10.1093/Gbe/Evx116 |
0.326 |
|
| 2017 |
Wang Z, Danziger SA, Heavner BD, Ma S, Smith JJ, Li S, Herricks T, Simeonidis E, Baliga NS, Aitchison JD, Price ND. Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast. Plos Computational Biology. 13: e1005489. PMID 28520713 DOI: 10.1371/Journal.Pcbi.1005489 |
0.379 |
|
| 2017 |
Thompson AW, Turkarslan S, Arens CE, López García de Lomana A, Raman AV, Stahl DA, Baliga NS. Robustness of a model microbial community emerges from population structure among single cells of a clonal population. Environmental Microbiology. PMID 28419704 DOI: 10.1111/1462-2920.13764 |
0.309 |
|
| 2017 |
Turkarslan S, Raman AV, Thompson AW, Arens CE, Gillespie MA, von Netzer F, Hillesland KL, Stolyar S, López García de Lomana A, Reiss DJ, Gorman-Lewis D, Zane GM, Ranish JA, Wall JD, Stahl DA, ... Baliga NS, et al. Mechanism for microbial population collapse in a fluctuating resource environment. Molecular Systems Biology. 13: 919. PMID 28320772 DOI: 10.15252/Msb.20167058 |
0.379 |
|
| 2016 |
Keller MP, Paul PK, Rabaglia ME, Stapleton DS, Schueler KL, Broman AT, Ye SI, Leng N, Brandon CJ, Neto EC, Plaisier CL, Simonett SP, Kebede MA, Sheynkman GM, Klein MA, ... Baliga NS, et al. The Transcription Factor Nfatc2 Regulates β-Cell Proliferation and Genes Associated with Type 2 Diabetes in Mouse and Human Islets. Plos Genetics. 12: e1006466. PMID 27935966 DOI: 10.1371/Journal.Pgen.1006466 |
0.343 |
|
| 2016 |
Patra B, Kon Y, Yadav G, Sevold AW, Frumkin JP, Vallabhajosyula RR, Hintze A, Østman B, Schossau J, Bhan A, Marzolf B, Tamashiro JK, Kaur A, Baliga NS, Grayhack EJ, et al. A genome wide dosage suppressor network reveals genomic robustness. Nucleic Acids Research. PMID 27899637 DOI: 10.1093/Nar/Gkw1148 |
0.436 |
|
| 2016 |
Plaisier CL, O'Brien S, Bernard B, Reynolds S, Simon Z, Toledo CM, Ding Y, Reiss DJ, Paddison PJ, Baliga NS. Causal Mechanistic Regulatory Network for Glioblastoma Deciphered Using Systems Genetics Network Analysis. Cell Systems. PMID 27426982 DOI: 10.1016/J.Cels.2016.06.006 |
0.379 |
|
| 2015 |
Toledo CM, Ding Y, Hoellerbauer P, Davis RJ, Basom R, Girard EJ, Lee E, Corrin P, Hart T, Bolouri H, Davison J, Zhang Q, Hardcastle J, Aronow BJ, Plaisier CL, ... Baliga NS, et al. Genome-wide CRISPR-Cas9 Screens Reveal Loss of Redundancy between PKMYT1 and WEE1 in Glioblastoma Stem-like Cells. Cell Reports. PMID 26673326 DOI: 10.1016/J.Celrep.2015.11.021 |
0.319 |
|
| 2015 |
López García de Lomana A, Schäuble S, Valenzuela J, Imam S, Carter W, Bilgin DD, Yohn CB, Turkarslan S, Reiss DJ, Orellana MV, Price ND, Baliga NS. Transcriptional program for nitrogen starvation-induced lipid accumulation in Chlamydomonas reinhardtii. Biotechnology For Biofuels. 8: 207. PMID 26633994 DOI: 10.1186/S13068-015-0391-Z |
0.381 |
|
| 2015 |
Ashworth J, Turkarslan S, Harris M, Orellana MV, Baliga NS. Pan-transcriptomic analysis identifies coordinated and orthologous functional modules in the diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum. Marine Genomics. PMID 26560047 DOI: 10.1016/J.Margen.2015.10.011 |
0.426 |
|
| 2015 |
Imam S, Schäuble S, Valenzuela J, López García de Lomana A, Carter W, Price ND, Baliga NS. A refined genome-scale reconstruction of Chlamydomonas metabolism provides a platform for systems-level analyses. The Plant Journal : For Cell and Molecular Biology. PMID 26485611 DOI: 10.1111/Tpj.13059 |
0.394 |
|
| 2015 |
Imam S, Schäuble S, Brooks AN, Baliga NS, Price ND. Data-driven integration of genome-scale regulatory and metabolic network models. Frontiers in Microbiology. 6: 409. PMID 25999934 DOI: 10.3389/Fmicb.2015.00409 |
0.363 |
|
| 2015 |
Turkarslan S, Peterson EJ, Rustad TR, Minch KJ, Reiss DJ, Morrison R, Ma S, Price ND, Sherman DR, Baliga NS. A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis. Scientific Data. 2: 150010. PMID 25977815 DOI: 10.1038/Sdata.2015.10 |
0.414 |
|
| 2015 |
Danziger SA, Reiss DJ, Ratushny AV, Smith JJ, Plaisier CL, Aitchison JD, Baliga NS. Bicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictions. Bmc Systems Biology. 9: S1. PMID 25881257 DOI: 10.1186/1752-0509-9-S2-S1 |
0.303 |
|
| 2015 |
Reiss DJ, Plaisier CL, Wu WJ, Baliga NS. cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism. Nucleic Acids Research. PMID 25873626 DOI: 10.1093/Nar/Gkv300 |
0.385 |
|
| 2015 |
Gomes-Filho JV, Zaramela LS, Italiani VC, Baliga NS, Vêncio RZ, Koide T. Sense overlapping transcripts in IS1341-type transposase genes are functional non-coding RNAs in archaea. Rna Biology. 12: 490-500. PMID 25806405 DOI: 10.1080/15476286.2015.1019998 |
0.423 |
|
| 2015 |
Minch KJ, Rustad TR, Peterson EJ, Winkler J, Reiss DJ, Ma S, Hickey M, Brabant W, Morrison B, Turkarslan S, Mawhinney C, Galagan JE, Price ND, Baliga NS, Sherman DR. The DNA-binding network of Mycobacterium tuberculosis. Nature Communications. 6: 5829. PMID 25581030 DOI: 10.1038/Ncomms6829 |
0.363 |
|
| 2014 |
Muller EE, Pinel N, Laczny CC, Hoopmann MR, Narayanasamy S, Lebrun LA, Roume H, Lin J, May P, Hicks ND, Heintz-Buschart A, Wampach L, Liu CM, Price LB, Gillece JD, ... ... Baliga NS, et al. Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage. Nature Communications. 5: 5603. PMID 25424998 DOI: 10.1038/Ncomms6603 |
0.345 |
|
| 2014 |
Plaisier CL, Lo FY, Ashworth J, Brooks AN, Beer KD, Kaur A, Pan M, Reiss DJ, Facciotti MT, Baliga NS. Evolution of context dependent regulation by expansion of feast/famine regulatory proteins. Bmc Systems Biology. 8: 122. PMID 25394904 DOI: 10.1186/S12918-014-0122-2 |
0.67 |
|
| 2014 |
Rustad TR, Minch KJ, Ma S, Winkler JK, Hobbs S, Hickey M, Brabant W, Turkarslan S, Price ND, Baliga NS, Sherman DR. Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network. Genome Biology. 15: 502. PMID 25380655 DOI: 10.1186/S13059-014-0502-3 |
0.375 |
|
| 2014 |
Ashworth J, Bernard B, Reynolds S, Plaisier CL, Shmulevich I, Baliga NS. Structure-based predictions broadly link transcription factor mutations to gene expression changes in cancers. Nucleic Acids Research. 42: 12973-83. PMID 25378323 DOI: 10.1093/Nar/Gku1031 |
0.331 |
|
| 2014 |
Ashworth J, Plaisier CL, Lo FY, Reiss DJ, Baliga NS. Inference of expanded Lrp-like feast/famine transcription factor targets in a non-model organism using protein structure-based prediction. Plos One. 9: e107863. PMID 25255272 DOI: 10.1371/Journal.Pone.0107863 |
0.491 |
|
| 2014 |
Zaramela LS, Vêncio RZ, ten-Caten F, Baliga NS, Koide T. Transcription start site associated RNAs (TSSaRNAs) are ubiquitous in all domains of life. Plos One. 9: e107680. PMID 25238539 DOI: 10.1371/Journal.Pone.0107680 |
0.356 |
|
| 2014 |
Peterson EJ, Reiss DJ, Turkarslan S, Minch KJ, Rustad T, Plaisier CL, Longabaugh WJ, Sherman DR, Baliga NS. A high-resolution network model for global gene regulation in Mycobacterium tuberculosis. Nucleic Acids Research. 42: 11291-303. PMID 25232098 DOI: 10.1093/Nar/Gku777 |
0.452 |
|
| 2014 |
Brooks AN, Reiss DJ, Allard A, Wu WJ, Salvanha DM, Plaisier CL, Chandrasekaran S, Pan M, Kaur A, Baliga NS. A system-level model for the microbial regulatory genome. Molecular Systems Biology. 10: 740. PMID 25028489 DOI: 10.15252/Msb.20145160 |
0.489 |
|
| 2014 |
Wurtmann EJ, Ratushny AV, Pan M, Beer KD, Aitchison JD, Baliga NS. An evolutionarily conserved RNase-based mechanism for repression of transcriptional positive autoregulation. Molecular Microbiology. 92: 369-82. PMID 24612392 DOI: 10.1111/Mmi.12564 |
0.398 |
|
| 2014 |
Beer KD, Wurtmann EJ, Pinel N, Baliga NS. Model organisms retain an "ecological memory" of complex ecologically relevant environmental variation. Applied and Environmental Microbiology. 80: 1821-31. PMID 24413600 DOI: 10.1128/Aem.03280-13 |
0.347 |
|
| 2014 |
Turkarslan S, Wurtmann EJ, Wu WJ, Jiang N, Bare JC, Foley K, Reiss DJ, Novichkov P, Baliga NS. Network portal: a database for storage, analysis and visualization of biological networks. Nucleic Acids Research. 42: D184-90. PMID 24271392 DOI: 10.1093/Nar/Gkt1190 |
0.331 |
|
| 2014 |
Danziger SA, Ratushny AV, Smith JJ, Saleem RA, Wan Y, Arens CE, Armstrong AM, Sitko K, Chen WM, Chiang JH, Reiss DJ, Baliga NS, Aitchison JD. Molecular mechanisms of system responses to novel stimuli are predictable from public data. Nucleic Acids Research. 42: 1442-60. PMID 24185701 DOI: 10.1093/Nar/Gkt938 |
0.438 |
|
| 2013 |
Ho Yoon S, Turkarslan S, Reiss DJ, Pan M, Burn JA, Costa KC, Lie TJ, Slagel J, Moritz RL, Hackett M, Leigh JA, Baliga NS. A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen Genome Research. 23: 1839-1851. PMID 24089473 DOI: 10.1101/Gr.153916.112 |
0.442 |
|
| 2013 |
Orellana MV, Pang WL, Durand PM, Whitehead K, Baliga NS. A role for programmed cell death in the microbial loop. Plos One. 8: e62595. PMID 23667496 DOI: 10.1371/Journal.Pone.0062595 |
0.302 |
|
| 2013 |
Ashworth J, Coesel S, Lee A, Armbrust EV, Orellana MV, Baliga NS. Genome-wide diel growth state transitions in the diatom Thalassiosira pseudonana. Proceedings of the National Academy of Sciences of the United States of America. 110: 7518-23. PMID 23596211 DOI: 10.1073/Pnas.1300962110 |
0.409 |
|
| 2013 |
Costa KC, Yoon SH, Pan M, Burn JA, Baliga NS, Leigh JA. Effects of H2 and formate on growth yield and regulation of methanogenesis in Methanococcus maripaludis. Journal of Bacteriology. 195: 1456-62. PMID 23335420 DOI: 10.1128/Jb.02141-12 |
0.306 |
|
| 2013 |
Rustad TR, Minch KJ, Brabant W, Winkler JK, Reiss DJ, Baliga NS, Sherman DR. Global analysis of mRNA stability in Mycobacterium tuberculosis. Nucleic Acids Research. 41: 509-17. PMID 23125364 DOI: 10.1093/Nar/Gks1019 |
0.315 |
|
| 2012 |
Muller EE, Pinel N, Gillece JD, Schupp JM, Price LB, Engelthaler DM, Levantesi C, Tandoi V, Luong K, Baliga NS, Korlach J, Keim PS, Wilmes P. Genome sequence of "Candidatus Microthrix parvicella" Bio17-1, a long-chain-fatty-acid-accumulating filamentous actinobacterium from a biological wastewater treatment plant. Journal of Bacteriology. 194: 6670-1. PMID 23144412 DOI: 10.1128/Jb.01765-12 |
0.334 |
|
| 2012 |
Edgar RS, Green EW, Zhao Y, van Ooijen G, Olmedo M, Qin X, Xu Y, Pan M, Valekunja UK, Feeney KA, Maywood ES, Hastings MH, Baliga NS, Merrow M, Millar AJ, et al. Peroxiredoxins are conserved markers of circadian rhythms. Nature. 485: 459-64. PMID 22622569 DOI: 10.1038/Nature11088 |
0.352 |
|
| 2012 |
Ashworth J, Wurtmann EJ, Baliga NS. Reverse engineering systems models of regulation: discovery, prediction and mechanisms. Current Opinion in Biotechnology. 23: 598-603. PMID 22209016 DOI: 10.1016/J.Copbio.2011.12.005 |
0.351 |
|
| 2011 |
Turkarslan S, Reiss DJ, Gibbins G, Su WL, Pan M, Bare JC, Plaisier CL, Baliga NS. Niche adaptation by expansion and reprogramming of general transcription factors. Molecular Systems Biology. 7: 554. PMID 22108796 DOI: 10.1038/Msb.2011.87 |
0.418 |
|
| 2011 |
Yoon SH, Reiss DJ, Bare JC, Tenenbaum D, Pan M, Slagel J, Moritz RL, Lim S, Hackett M, Menon AL, Adams MW, Barnebey A, Yannone SM, Leigh JA, Baliga NS. Parallel evolution of transcriptome architecture during genome reorganization. Genome Research. 21: 1892-904. PMID 21750103 DOI: 10.1101/Gr.122218.111 |
0.477 |
|
| 2011 |
Plaisier CL, Bare JC, Baliga NS. miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling. Nucleic Acids Research. 39: W125-31. PMID 21602264 DOI: 10.1093/Nar/Gkr374 |
0.305 |
|
| 2011 |
Brooks AN, Turkarslan S, Beer KD, Lo FY, Baliga NS. Adaptation of cells to new environments. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 3: 544-61. PMID 21197660 DOI: 10.1002/Wsbm.136 |
0.368 |
|
| 2011 |
Schmid AK, Pan M, Sharma K, Baliga NS. Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon. Nucleic Acids Research. 39: 2519-33. PMID 21109526 DOI: 10.1093/Nar/Gkq1211 |
0.344 |
|
| 2010 |
Kaur A, Van PT, Busch CR, Robinson CK, Pan M, Pang WL, Reiss DJ, DiRuggiero J, Baliga NS. Coordination of frontline defense mechanisms under severe oxidative stress. Molecular Systems Biology. 6: 393. PMID 20664639 DOI: 10.1038/Msb.2010.50 |
0.345 |
|
| 2010 |
Bare JC, Koide T, Reiss DJ, Tenenbaum D, Baliga NS. Integration and visualization of systems biology data in context of the genome. Bmc Bioinformatics. 11: 382. PMID 20642854 DOI: 10.1186/1471-2105-11-382 |
0.391 |
|
| 2010 |
Facciotti MT, Pang WL, Lo FY, Whitehead K, Koide T, Masumura K, Pan M, Kaur A, Larsen DJ, Reiss DJ, Hoang L, Kalisiak E, Northen T, Trauger SA, Siuzdak G, ... Baliga NS, et al. Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis. Bmc Systems Biology. 4: 64. PMID 20470417 DOI: 10.1186/1752-0509-4-64 |
0.692 |
|
| 2009 |
Koide T, Reiss DJ, Bare JC, Pang WL, Facciotti MT, Schmid AK, Pan M, Marzolf B, Van PT, Lo FY, Pratap A, Deutsch EW, Peterson A, Martin D, Baliga NS. Prevalence of transcription promoters within archaeal operons and coding sequences. Molecular Systems Biology. 5: 285. PMID 19536208 DOI: 10.1038/Msb.2009.42 |
0.727 |
|
| 2009 |
Schmid AK, Reiss DJ, Pan M, Koide T, Baliga NS. A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability. Molecular Systems Biology. 5: 282. PMID 19536205 DOI: 10.1038/Msb.2009.40 |
0.395 |
|
| 2009 |
Whitehead K, Pan M, Masumura K, Bonneau R, Baliga NS. Diurnally entrained anticipatory behavior in archaea. Plos One. 4: e5485. PMID 19424498 DOI: 10.1371/Journal.Pone.0005485 |
0.357 |
|
| 2009 |
Koide T, Pang WL, Baliga NS. The role of predictive modelling in rationally re-engineering biological systems. Nature Reviews. Microbiology. 7: 297-305. PMID 19252506 DOI: 10.1038/Nrmicro2107 |
0.336 |
|
| 2008 |
Van PT, Schmid AK, King NL, Kaur A, Pan M, Whitehead K, Koide T, Facciotti MT, Goo YA, Deutsch EW, Reiss DJ, Mallick P, Baliga NS. Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage. Journal of Proteome Research. 7: 3755-64. PMID 18652504 DOI: 10.1021/Pr800031F |
0.62 |
|
| 2008 |
Rubio ED, Reiss DJ, Welcsh PL, Disteche CM, Filippova GN, Baliga NS, Aebersold R, Ranish JA, Krumm A. CTCF physically links cohesin to chromatin. Proceedings of the National Academy of Sciences of the United States of America. 105: 8309-14. PMID 18550811 DOI: 10.1073/Pnas.0801273105 |
0.327 |
|
| 2008 |
Baliga NS. Systems biology. The scale of prediction. Science (New York, N.Y.). 320: 1297-8. PMID 18535232 DOI: 10.1126/Science.1159485 |
0.321 |
|
| 2008 |
Reiss DJ, Facciotti MT, Baliga NS. Model-based deconvolution of genome-wide DNA binding. Bioinformatics (Oxford, England). 24: 396-403. PMID 18056063 DOI: 10.1093/Bioinformatics/Btm592 |
0.682 |
|
| 2008 |
Johnson MH, Facciotti MT, Reiss DJ, Whitehead K, Schmid A, Kaur A, Pan M, Shannon P, Tenenbaum D, Bonneau R, Baliga NS. QS437. Integrated Biological and Computational Analysis of Important But Largely Under-Studied Organisms Journal of Surgical Research. 144: 441. DOI: 10.1016/J.Jss.2007.12.695 |
0.642 |
|
| 2007 |
Bonneau R, Facciotti MT, Reiss DJ, Schmid AK, Pan M, Kaur A, Thorsson V, Shannon P, Johnson MH, Bare JC, Longabaugh W, Vuthoori M, Whitehead K, Madar A, Suzuki L, ... ... Baliga NS, et al. A predictive model for transcriptional control of physiology in a free living cell. Cell. 131: 1354-65. PMID 18160043 DOI: 10.1016/J.Cell.2007.10.053 |
0.741 |
|
| 2007 |
Schmid AK, Reiss DJ, Kaur A, Pan M, King N, Van PT, Hohmann L, Martin DB, Baliga NS. The anatomy of microbial cell state transitions in response to oxygen. Genome Research. 17: 1399-413. PMID 17785531 DOI: 10.1101/Gr.6728007 |
0.368 |
|
| 2007 |
Facciotti MT, Reiss DJ, Pan M, Kaur A, Vuthoori M, Bonneau R, Shannon P, Srivastava A, Donohoe SM, Hood LE, Baliga NS. General transcription factor specified global gene regulation in archaea. Proceedings of the National Academy of Sciences of the United States of America. 104: 4630-5. PMID 17360575 DOI: 10.1073/Pnas.0611663104 |
0.745 |
|
| 2006 |
Whitehead K, Kish A, Pan M, Kaur A, Reiss DJ, King N, Hohmann L, DiRuggiero J, Baliga NS. An integrated systems approach for understanding cellular responses to gamma radiation. Molecular Systems Biology. 2: 47. PMID 16969339 DOI: 10.1038/Msb4100091 |
0.356 |
|
| 2006 |
Kaur A, Pan M, Meislin M, Facciotti MT, El-Gewely R, Baliga NS. A systems view of haloarchaeal strategies to withstand stress from transition metals. Genome Research. 16: 841-54. PMID 16751342 DOI: 10.1101/Gr.5189606 |
0.629 |
|
| 2006 |
Reiss DJ, Baliga NS, Bonneau R. Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. Bmc Bioinformatics. 7: 280. PMID 16749936 DOI: 10.1186/1471-2105-7-280 |
0.374 |
|
| 2006 |
Bonneau R, Reiss DJ, Shannon P, Facciotti M, Hood L, Baliga NS, Thorsson V. The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biology. 7: R36. PMID 16686963 DOI: 10.1186/Gb-2006-7-5-R36 |
0.728 |
|
| 2006 |
Shannon PT, Reiss DJ, Bonneau R, Baliga NS. The Gaggle: an open-source software system for integrating bioinformatics software and data sources. Bmc Bioinformatics. 7: 176. PMID 16569235 DOI: 10.1186/1471-2105-7-176 |
0.3 |
|
| 2005 |
Iyer R, Baliga NS, Camilli A. Catabolite control protein A (CcpA) contributes to virulence and regulation of sugar metabolism in Streptococcus pneumoniae. Journal of Bacteriology. 187: 8340-9. PMID 16321938 DOI: 10.1128/Jb.187.24.8340-8349.2005 |
0.349 |
|
| 2004 |
Baliga NS, Bonneau R, Facciotti MT, Pan M, Glusman G, Deutsch EW, Shannon P, Chiu Y, Weng RS, Gan RR, Hung P, Date SV, Marcotte E, Hood L, Ng WV. Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Research. 14: 2221-34. PMID 15520287 DOI: 10.1101/Gr.2700304 |
0.799 |
|
| 2004 |
Weston AD, Baliga NS, Bonneau R, Hood L. Systems approaches applied to the study of Saccharomyces cerevisiae and Halobacterium sp. Cold Spring Harbor Symposia On Quantitative Biology. 68: 345-57. PMID 15338636 DOI: 10.1101/Sqb.2003.68.345 |
0.468 |
|
| 2004 |
Bonneau R, Baliga NS, Deutsch EW, Shannon P, Hood L. Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1. Genome Biology. 5: R52. PMID 15287974 DOI: 10.1186/Gb-2004-5-8-R52 |
0.554 |
|
| 2004 |
Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1. Genome Research. 14: 1025-35. PMID 15140832 DOI: 10.1101/Gr.1993504 |
0.568 |
|
| 2004 |
Facciotti MT, Cheung VS, Lunde CS, Rouhani S, Baliga NS, Glaeser RM. Specificity of Anion Binding in the Substrate Pocket of Bacteriorhodopsin Biochemistry. 43: 4934-4943. PMID 15109251 DOI: 10.1021/Bi035757S |
0.689 |
|
| 2004 |
Goo YA, Roach J, Glusman G, Baliga NS, Deutsch K, Pan M, Kennedy S, DasSarma S, Ng WV, Hood L. Low-pass sequencing for microbial comparative genomics. Bmc Genomics. 5: 3. PMID 14718067 DOI: 10.1186/1471-2164-5-3 |
0.77 |
|
| 2004 |
Facciotti MT, Bonneau R, Hood L, Baliga NS. Systems biology experimental design - Considerations for building predictive gene regulatory network models for prokaryotic systems Current Genomics. 5: 527-544. DOI: 10.2174/1389202043348850 |
0.698 |
|
| 2003 |
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research. 13: 2498-504. PMID 14597658 DOI: 10.1101/Gr.1239303 |
0.358 |
|
| 2003 |
Goo YA, Yi EC, Baliga NS, Tao WA, Pan M, Aebersold R, Goodlett DR, Hood L, Ng WV. Proteomic analysis of an extreme halophilic archaeon, Halobacterium sp. NRC-1. Molecular & Cellular Proteomics : McP. 2: 506-24. PMID 12872007 DOI: 10.1074/Mcp.M300044-Mcp200 |
0.723 |
|
| 2002 |
Baliga NS, Pan M, Goo YA, Yi EC, Goodlett DR, Dimitrov K, Shannon P, Aebersold R, Ng WV, Hood L. Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach. Proceedings of the National Academy of Sciences of the United States of America. 99: 14913-8. PMID 12403819 DOI: 10.1073/Pnas.192558999 |
0.737 |
|
| 2001 |
Dassarma S, Kennedy SP, Berquist B, Victor Ng W, Baliga NS, Spudich JL, Krebs MP, Eisen JA, Johnson CH, Hood L. Genomic perspective on the photobiology of Halobacterium species NRC-1, a phototrophic, phototactic, and UV-tolerant haloarchaeon. Photosynthesis Research. 70: 3-17. PMID 16228359 DOI: 10.1023/A:1013879706863 |
0.771 |
|
| 2001 |
Baliga NS. Promoter analysis by saturation mutagenesis. Biological Procedures Online. 3: 64-69. PMID 12734578 DOI: 10.1251/Bpo24 |
0.415 |
|
| 2001 |
Baliga NS, Kennedy SP, Ng WV, Hood L, DasSarma S. Genomic and genetic dissection of an archaeal regulon. Proceedings of the National Academy of Sciences of the United States of America. 98: 2521-5. PMID 11226271 DOI: 10.1073/Pnas.051632498 |
0.79 |
|
| 2000 |
Ng WV, Kennedy SP, Mahairas GG, Berquist B, Pan M, Shukla HD, Lasky SR, Baliga NS, Thorsson V, Sbrogna J, Swartzell S, Weir D, Hall J, Dahl TA, Welti R, et al. Genome sequence of Halobacterium species NRC-1. Proceedings of the National Academy of Sciences of the United States of America. 97: 12176-81. PMID 11016950 DOI: 10.1073/Pnas.190337797 |
0.769 |
|
| 2000 |
Baliga NS, Goo YA, Ng WV, Hood L, Daniels CJ, DasSarma S. Is gene expression in Halobacterium NRC-1 regulated by multiple TBP and TFB transcription factors? Molecular Microbiology. 36: 1184-5. PMID 10844702 DOI: 10.1046/J.1365-2958.2000.01916.X |
0.772 |
|
| 2000 |
Baliga NS, DasSarma S. Saturation mutagenesis of the haloarchaeal bop gene promoter: identification of DNA supercoiling sensitivity sites and absence of TFB recognition element and UAS enhancer activity. Molecular Microbiology. 36: 1175-83. PMID 10844701 DOI: 10.1046/J.1365-2958.2000.01915.X |
0.625 |
|
| 1999 |
Baliga NS, DasSarma S. Saturation mutagenesis of the TATA box and upstream activator sequence in the haloarchaeal bop gene promoter. Journal of Bacteriology. 181: 2513-8. PMID 10198017 DOI: 10.1128/Jb.181.8.2513-2518.1999 |
0.634 |
|
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